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Thermal Motion (thermal + motion)
Selected AbstractsTemperature effects on the UV,Vis electronic spectrum of trans-stilbeneINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001S. P. Kwasniewski Abstract The ultraviolet (UV),Visible absorption spectrum of trans-stilbene (tS) is computed at different temperatures by coupling molecular dynamics (MD) simulations with the classical MM3 force field to ZINDO/S-CIS calculations of vertical excitation energies and transition dipole moments. The selection of a large number of structures along the MD trajectories enables a consistent treatment of temperature effects in the vacuum, whereas the ZINDO/S-CIS calculations permit a reliable treatment of electron correlation and relaxation, taking account of multistate interactions in the final state. Thermal motions are found to alter very differently the width and shape of bands. Structural alterations such as the stretching and the torsion of the vinyl single and double bonds very strongly influence the appearance of the first valence state, pertaining to the highest occupied and lowest unoccupied molecular orbital (HOMO,LUMO) transition. At temperatures less than 400 K, these are found to yield a merely Gaussian and very pronounced thermal broadening of the related band (A), up to nearly 30 nm, together with a minor blue shift of its maximum ,max. In contrast, a red shift by several nanometers occurs due to thermal motions for the remaining three valence bands. As can be expected, the broadening intensifies at higher temperatures, and for the A-band, becomes markedly asymmetric when T exceeds 400 K. The combination of MD(MM3) and ZINDO/S-CIS computations enables also consistent calculations of hot bands, which are forbidden by symmetry at 0 K. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] The effect of water content on proton transport in polymer electrolyte membranesFUEL CELLS, Issue 3-4 2002P. Commer Abstract We investigate proton transport in a polymer electrolyte membrane using continuum theory and molecular dynamics (MD) computer simulations. Specifically our goal is to understand the possible molecular origin of the effect of water content on the activation energy (AE) and pre-exponential factor of proton conductivity, in comparison with experimental observations reported for Nafion, where a decrease of AE with increasing water content has been observed. We study proton diffusion in a single pore, using a slab-like model. We find that although the average proton diffusion coefficient is several times smaller in a narrow pore than in a wide water-rich pore, its AE is almost unaffected by the pore width. This contradicts an earlier proposed conjecture that the sizable Coulomb potential energy barriers near the lattice of immobile point-like SO3, groups increase the AE in a narrow pore. Here we show that these barriers become smeared out by thermal motion of SO3, groups and by the spatial charge distribution over their atoms. This effect strongly diminishes the variation of the AE with pore width, which is also found in MD simulations. The pre-exponential factor for the diffusion process, however, decreases, indicating a limited number of pathways for proton transfer and the freezing out of degrees of freedom that contribute to the effective frequency of transfer. Decreasing the pore size diminishes bulk-like water regions in the pore, with only less mobile surface water molecules remaining. This hampers proton transfer. The increase of AE takes place only if the thermal motion of the SO3, head groups freezes out simultaneously with decreasing water content, but the effect is not profound. The stronger effect observed experimentally may thus be associated with some other rate-determining consecutive process, concerned with polymer dynamics, such as opening and closing of connections (bridges) between aqueous domains in the membrane under low water content. [source] Energetic materials: variable-temperature crystal structure of ,-NTOJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003Nadezhda B. Bolotina The crystal structure of the metastable , form of 5-nitro-2,4-dihydro-3H -1,2,4-triazol-3-one (,-NTO, monoclinic, P21/c) has been investigated at five temperatures in the range 100,298,K using single-crystal X-ray diffraction techniques. The second-rank thermal expansion tensor has been determined to describe thermal behavior of the crystal. The most significant thermal expansion is in a plane, which is almost perpendicular to the planes of all the NTO molecules. Perpendicular to the plane of maximal thermal expansion, a modest thermal contraction takes place. Both thermal expansion and contraction of the crystal lattice indicate anharmonicity of the atomic thermal motion. The experimental thermal variation of the unit-cell parameters is in qualitative agreement with that previously obtained from molecular dynamics calculations. Rigid-body analysis of the molecular thermal motion was performed using the libration and translation second-rank tensors. Although the translation part of the thermal motion is not strongly anisotropic, the largest displacements of the NTO molecules are oriented in the plane of maximal thermal expansion of the crystal and have significant anharmonic components. The libration motion is more anisotropic, and the largest libration as well as the largest translation principal axes are directed along the C5,N5 bond in each NTO molecule. [source] Analyzing single-molecule manipulation experimentsJOURNAL OF MOLECULAR RECOGNITION, Issue 5 2009Christopher P. Calderon Abstract Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.g., inherent thermal motion, instrument measurement error, etc. The primary focus of this paper is a methodology that uses time domain based methods to extract the effective molecular friction from single-molecule pulling data. We studied molecules composed of eight tandem repeat titin I27 domains, but the modeling approaches have applicability to other single-molecule mechanical studies. The merits and challenges associated with applying such a computational approach to existing single-molecule manipulation data are also discussed. Copyright © 2009 John Wiley & Sons, Ltd. [source] Influence of thermal motion on 1H chemical shifts in proteins: the case of bovine pancreatic trypsin inhibitorJOURNAL OF PEPTIDE SCIENCE, Issue 3 2001Bernard Busetta Abstract The possible influence of thermal motion on 1H chemical shifts is discussed for a small stable protein, the bovine pancreatic Kunitz trypsin inhibitor (BPTI). The thermal effects on the aromatic side chains and on the backbone are treated separately. The thermal motion of the aromatic side chains is accounted for in terms of their rotation around the C,C, bond and the motion of each individual proton is interpreted as a ratio between the amount of ordered and quite disordered states. The influence of hydrogen bonds is introduced as an extra contribution to the chemical shifts of the bonded proton. Their contribution to the chemical shifts resulting from the polarization of the peptide bond is investigated, as is their influence on local flexibility. Finally, the relative importance of each contribution to the chemical shift information is compared. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd. [source] Radiation damage of protein crystals at cryogenic temperatures between 40,K and 150,KJOURNAL OF SYNCHROTRON RADIATION, Issue 4 2002Tsu-Yi Teng X-ray radiation damage of lysozyme single crystals by an intense monochromatic beam from the Advanced Photon Source is studied at cryogenic temperatures between 40,K and 150,K. The results confirm that primary radiation damage is both linearly dependent on the X-ray dose and independent of temperature. The upper limit for the primary radiation damage observed in our previous study [Teng & Moffat (2000), J. Synchrotron Rad. 7, 313317] holds over the wider temperature range of this study. The X-ray diffraction quality of the data acquired at 40,K is superior to those at 100,K, apparently due to temperature dependence of secondary and tertiary radiation damage and to reduced thermal motion. [source] Baryon loading and the Weibel instability in gamma-ray burstsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2006M. Fiore ABSTRACT The dynamics of two counter-streaming electron,positron,ion unmagnetized plasma shells with zero net charge is analysed in the context of magnetic field generation in gamma-ray burst internal shocks due to the Weibel instability. The effects of large thermal motion of plasma particles, arbitrary mixture of plasma species and space charge effects are taken into account. We show that, although thermal effects slow down the instability, baryon loading leads to a non-negligible growth rate even for large temperatures and different shell velocities, thus guaranteeing the robustness and the occurrence of the Weibel instability for a wide range of scenarios. [source] Dynamic Light Scattering for the Characterization of Polydisperse Fractal Systems: I. Simulation of the Diffusional BehaviorPARTICLE & PARTICLE SYSTEMS CHARACTERIZATION, Issue 1 2008Uwe Kätzel Abstract Dynamic light scattering (DLS) is a method used to size nanoscale and submicron particles by measuring their thermal motion (diffusion) in a liquid environment. The measured diffusion coefficients are related to the hydrodynamic particle size via the Stokes-Einstein equation. This paper addresses the application of DLS for the characterization of diluted suspensions of pyrogenic silica, which consist of polydisperse fractal-like aggregates composed of sintered spherical primary particles. Simulations are employed to establish a relationship between the structural properties of the aggregates and their diffusional behavior. Therefore, an algorithm is developed that enables the generation of aggregates with a tunable fractal dimension and an arbitrary number of primary particles. The results provide evidence that the hydrodynamic radii show a different scaling compared to the structural radius of gyration, which is of great relevance for the interpretation of DLS results. In addition, the influence of rotational diffusion has to be accounted for in the measurements. [source] Multipole electron-density modelling of synchrotron powder diffraction data: the case of diamondACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2010H. Svendsen Accurate structure factors are extracted from synchrotron powder diffraction data measured on crystalline diamond based on a novel multipole model division of overlapping reflection intensities. The approach limits the spherical-atom bias in structure factors extracted from overlapping powder data using conventional spherical-atom Rietveld refinement. The structure factors are subsequently used for multipole electron-density modelling, and both the structure factors and the derived density are compared with results from ab initio theoretical calculations. Overall, excellent agreement is obtained between experiment and theory, and the study therefore demonstrates that synchrotron powder diffraction can indeed provide accurate structure-factor values based on data measured in minutes with limited sample preparation. Thus, potential systematic errors such as extinction and twinning commonly encountered in single-crystal studies of small-unit-cell inorganic structures can be overcome with synchrotron powder diffraction. It is shown that the standard Hansen,Coppens multipole model is not flexible enough to fit the static theoretical structure factors, whereas fitting of thermally smeared structure factors has much lower residuals. If thermally smeared structure factors (experimental or theoretical) are fitted with a slightly wrong radial model (s2p2 instead of sp3) the radial scaling parameters (`,' parameters) are found to be inadequate and the `error' is absorbed into the atomic displacement parameter. This directly exposes a correlation between electron density and thermal parameters even for a light atom such as carbon, and it also underlines that in organic systems proper deconvolution of thermal motion is important for obtaining correct static electron densities. [source] EXAFS studies of lattice dynamics and thermal expansionPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 11 2004P. Fornasini Abstract Accurate temperature-dependent EXAFS measurements can give original information on the correlation of thermal motion in crystals, not only along the bond direction (parallel Mean Square Relative Displacement, MSRD), but also within the perpendicular plane (perpendicular MSRD). This potential is demonstrated by the results obtained for copper and germanium, taken as model systems. Possible applications for investigating on the local origin of Negative Thermal Expansion are being supported by measurements on crystals with the cuprite structure. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structuresACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2007Bartosz Zarychta With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diffraction data. The library transfer is applied automatically in the MoPro software suite to peptide and protein structures measured at atomic resolution. The transferred multipolar parameters are kept fixed while the positional and thermal parameters are refined. This enables a proper deconvolution of thermal motion and valence-electron-density redistributions, even when the diffraction data do not extend to subatomic resolution. The use of the experimental library multipolar atom model (ELMAM) also has a major impact on crystallographic structure modelling in the case of small-molecule crystals at atomic resolution. Compared to a spherical-atom model, the library transfer results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. Upon transfer, crystallographic statistics of fit are improved, particularly free R factors, and residual electron-density maps are cleaner. [source] Polarization anisotropy of X-ray atomic factors and `forbidden' resonant reflectionsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2005Vladimir E. Dmitrienko Symmetry and physical aspects of `forbidden' reflections excited by a local polarization anisotropy of the X-ray susceptibility are surveyed. Such reflections are observed near absorption edges where the anisotropy is caused by distortions of the atomic electronic states owing to interaction with neighbouring atoms. As a consequence, they allow for extracting nontrivial information about the resonant atom's local environment and their physical conditions. The unusual polarization properties of the considered reflections are helpful to distinguish them from other types of `forbidden' reflections. When such reflections are excited, it is, for example, possible to determine not only the intrinsic anisotropy of an atomic form factor but also additional anisotropy induced by thermal motion, point defects and/or incommensurate modulations. Even the local `chirality' of atoms in centrosymmetric crystals is accessible. Unsolved key problems and possible future developments are addressed. [source] X-ray diffraction by a crystal in a permanent external electric field: general considerationsACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2005Semen V. Gorfman The variations of X-ray diffraction intensities from a crystal in the presence of a permanent external electric field is modeled analytically using a first-order stationary perturbation theory. The change in a crystal, induced by an external electric field, is separated into two contributions. The first one is related to a pure polarization of an electron subsystem, while the second contribution can be reduced to the displacements of the rigid pseudoatoms from their equilibrium positions. It is shown that a change of the X-ray diffraction intensities mainly originates from the second contribution, while the influence of the pure polarization of a crystal electron subsystem is negligibly small. The quantities restored from an X-ray diffraction experiment in the presence of an external electric field were analyzed in detail in terms of a rigid pseudoatomic model of electron density and harmonic approximation for the atomic thermal motion. Explicit relationships are derived that link the properties of phonon spectra with E -field-induced variations of a structure factor, pseudoatomic displacements and piezoelectric strains. The displacements can be numerically estimated using a model of independent atomic motion if the Debye,Waller factors and pseudoatomic charges are known either from a previous single-crystal X-ray diffraction study or from density functional theory calculations. The above estimations can be used to develop an optimum strategy for a data collection that avoids the measurements of reflections insensitive to the electric-field-induced variations. [source] The invariom model and its application: refinement of d,l -serine at different temperatures and resolutionACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2005B. Dittrich Three X-ray data sets of the same d,l -serine crystal were measured at temperatures of 298, 100 and 20,K. These data were then evaluated using invarioms and the Hansen & Coppens aspherical-atom model. Multipole populations for invarioms, which are pseudoatoms that remain approximately invariant in an intermolecular transfer, were theoretically predicted using different density functional theorem (DFT) basis sets. The invariom parameters were kept fixed and positional and thermal parameters were refined to compare the fitting against the multi-temperature data at different resolutions. The deconvolution of thermal motion and electron density with respect to data resolution was studied by application of the Hirshfeld test. Above a resolution of sin,/,,,,0.55,Å,1, or d,,,0.9,Å, this test was fulfilled. When the Hirshfeld test is fulfilled, a successful modeling of the aspherical electron density with invarioms is achieved, which was proven by Fourier methods. Molecular geometry improves, especially for H atoms, when using the invariom method compared to the independent-atom model, as a comparison with neutron data shows. Based on this example, the general applicability of the invariom concept to organic molecules is proven and the aspherical density modeling of a larger biomacromolecule is within reach. [source] On the influence of thermal motion on the crystal structures and polymorphism of even n -alkanesACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002Jacco Van De Streek Discrepancies between the crystal structures of short n -alkanes as obtained from experiment and as obtained from molecular mechanics tended to worsen at longer chain lengths. The same holds for the relative stabilities of the two experimentally observed polymorphs. In this paper it is argued that the discrepancies are caused by thermal effects, and that the triclinic polymorph is the most stable polymorph for all chain lengths at 0,K. A phase transition is predicted but has yet to be found experimentally. Current force fields cannot reproduce the experimental observations without explicit introduction of temperature by means of molecular dynamics. [source] Single crystal structure and molecular dynamics analysis of a myo -inositol derivativeACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2000Jan Dillen The crystal structure of 5- O - tert -butyldimethylsilyl-3,4- O -carbonyl-1,2- O -cyclohexylidene-2-oxo-3-oxa-4-bornanylcarbonyl- d - myo -inositol has been studied by single-crystal X-ray diffraction at both room temperature and 173,K. At room temperature, the tert -butyldimethylsilyl group exhibits dynamical disorder. A molecular dynamics simulation was used to model the disorder and this indicates that the group librates between two stable conformations in the crystal. Approximate relative energies of the different forms and energy barriers for the transition were obtained by empirical force field methods. Calculations of the thermal motion of the atoms are in good qualitative, but fair to poor quantitative agreement with the X-ray data. [source] Extracting charge density distributions from diffraction data: a model study on ureaACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2000R. Y. De Vries The quality of the extraction of electron density distributions by means of a multipole refinement method is investigated. Structure factors of the urea crystal have been obtained from an electron density distribution (EDD) resulting from a density function calculation with the CRYSTAL95 package. To account for the thermal motion of the atoms, the stockholder-partioned densities of the atoms have been convoluted with thermal smearing functions, which were obtained from a neutron diffraction experiment. A POP multipole refinement yielded a good fit, R = 0.6%. This disagreement factor is based on magnitudes only. Comparison with the original structure factors gave a disagreement of 0.8% owing to differences in magnitude and phase. The fitted EDD still showed all the characteristics of the interaction density. After random errors corresponding to the experimental situation were added to the structure factors, the refinement was repeated. The fit was R = 1.1%. This time the resulting interaction density was heavily deformed. Repetition with another set of random errors from the same distribution yielded a widely different interaction density distribution. The conclusion is that interaction densities cannot be obtained from X-ray diffraction data on non-centrosymmetric crystals. [source] Di-,-oxido-bis{bis[N,N,-bis(2-pyridylmethyl)ethane-1,2-diamine]manganese(III,IV)} tris(perchlorate) hexahydrate: clarification of an order,disorder phase transitionACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009Anne Nielsen The title compound, [Mn2O2(C14H18N4)2](ClO4)3·6H2O, contains a mixed-valent MnIII/MnIV complex. In accordance with a previous report [Collins, Hodgson, Michelsen & Towle (1987). J. Chem. Soc. Chem. Commun. pp. 1659,1660], the structure at 295,K is best described in the space group C2/c, with the complex exhibiting twofold rotational symmetry, and with half site occupancy for one perchlorate anion and several solvent water molecules. At 180,K, the structure is ordered in the subgroup P21/n and is clearly shown to be a hexahydrate, rather than the previously reported trihydrate. The origin of the order,disorder phase transition lies in the thermal motion of the perchlorate anions. [source] Thermal dynamics at surfacesANNALEN DER PHYSIK, Issue 10-11 2009H. Brune Abstract The present paper describes what happens at the surface of a crystal as its temperature steadily increases from zero Kelvin close to the bulk melting temperature. We treat thermal motion, such as the diffusion of individual adatoms establishing mass transport, the formation of adatom or vacancy gases coexisting with islands or steps of the condensed phase, surface phonons and the anharmonicity of the surface potential being markedly different from the one in bulk, as well as thermally induced reconstructions, surface roughening, and finally surface melting, which usually well precedes bulk melting. The paper intends to give an overview with references to the original and review literature. [source] Thermal dynamics at surfacesANNALEN DER PHYSIK, Issue 10-11 2009H. Brune Abstract The present paper describes what happens at the surface of a crystal as its temperature steadily increases from zero Kelvin close to the bulk melting temperature. We treat thermal motion, such as the diffusion of individual adatoms establishing mass transport, the formation of adatom or vacancy gases coexisting with islands or steps of the condensed phase, surface phonons and the anharmonicity of the surface potential being markedly different from the one in bulk, as well as thermally induced reconstructions, surface roughening, and finally surface melting, which usually well precedes bulk melting. The paper intends to give an overview with references to the original and review literature. [source] Feedback control in flashing ratchets,ANNALEN DER PHYSIK, Issue 2-3 2008E.M. Craig Abstract A flashing ratchet uses a time-dependent, spatially periodic, asymmetric potential to rectify thermal motion of Brownian particles. Here we review approaches to improve the particle flux in this type of Brownian motor by feedback strategies that switch the potential based on the instantaneous particle distribution. We review strategies that are based on the force experienced by the particles, and introduce a new feedback strategy that is based on the expected displacement that can be achieved. Langevin dynamics simulations show that this maximum net displacement strategy performs better than force-based strategies in the limit of very small particle numbers and not too high temperatures. We also review the effects of time delay and noisy channels on feedback control, and perform a feasibility analysis of an experimental system that can realize feedback control using a computer-controlled, scanning-line optical trap and suspended microspheres. [source] Orientational disorder in 4-chloronitrobenzeneACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2008Lynne H. Thomas The crystal structure of 4-chloronitrobenzene, C6H4ClNO2, a material that exhibits disorder in the solid state, is re-examined using multiple-temperature single-crystal X-ray diffraction. Our results show a marked improvement on previous crystal structure determinations and our comprehensive multiple temperature measurements help to rationalize the structural anomalies. 4-Chloronitrobenzene exhibits twofold orientational disorder of the NO2/Cl substituents, with the molecule lying across an inversion centre. There is also evidence of large thermal motion, which exists at all temperatures and reflects the presence of significant disorder in this material. The nitro group shows possible libration, with one O atom exhibiting larger thermal motion than the other across the whole temperature range. This is explained by a difference in hydrogen-bonding environment. [source] Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Anna S. Gardberg The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65,Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3 -protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1,Å resolution X-ray diffraction studies of the same protein at both RT and 100,K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the , level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65,Å resolution RT neutron data for perdeuterated rubredoxin are ,8 times more likely overall to provide high-confidence positions for D atoms than 1.1,Å resolution X-ray data at 100,K or RT. At or above the 1.0, level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1,Å resolution 100,K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0, level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only. [source] Temperature effects on the UV,Vis electronic spectrum of trans-stilbeneINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001S. P. Kwasniewski Abstract The ultraviolet (UV),Visible absorption spectrum of trans-stilbene (tS) is computed at different temperatures by coupling molecular dynamics (MD) simulations with the classical MM3 force field to ZINDO/S-CIS calculations of vertical excitation energies and transition dipole moments. The selection of a large number of structures along the MD trajectories enables a consistent treatment of temperature effects in the vacuum, whereas the ZINDO/S-CIS calculations permit a reliable treatment of electron correlation and relaxation, taking account of multistate interactions in the final state. Thermal motions are found to alter very differently the width and shape of bands. Structural alterations such as the stretching and the torsion of the vinyl single and double bonds very strongly influence the appearance of the first valence state, pertaining to the highest occupied and lowest unoccupied molecular orbital (HOMO,LUMO) transition. At temperatures less than 400 K, these are found to yield a merely Gaussian and very pronounced thermal broadening of the related band (A), up to nearly 30 nm, together with a minor blue shift of its maximum ,max. In contrast, a red shift by several nanometers occurs due to thermal motions for the remaining three valence bands. As can be expected, the broadening intensifies at higher temperatures, and for the A-band, becomes markedly asymmetric when T exceeds 400 K. The combination of MD(MM3) and ZINDO/S-CIS computations enables also consistent calculations of hot bands, which are forbidden by symmetry at 0 K. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Solvent models for protein,ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2001Linda Yu Zhang Abstract Solvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions, but they have not been parameterized on such complex problems, and therefore, it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models. The solvation free energy calculations are more than 103 faster using the Surface Generalized Born implicit solvent model compared to FEP simulations with explicit solvent. For some of the electrostatic calculations needed to estimate the binding free energy, there is near quantitative agreement between the explicit and implicit solvent model results; overall, the qualitative trends in the binding predicted by the explicit solvent FEP simulations are reproduced by the implicit solvent model. With an appropriate choice of reference system based on the binding of the discharged ligand, electrostatic interactions are found to enhance the binding affinity because the favorable Coulomb interaction energy between the ligand and protein more than compensates for the unfavorable free energy cost of partially desolvating the ligand upon binding. Some of the effects of protein flexibility and thermal motions on charging the peptide in the solvated complex are also considered. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 591,607, 2001 [source] Towards the best model for H atoms in experimental charge-density refinementACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009Anna A. Hoser The consequences of different treatments of H atoms in experimental charge-density studies are discussed. Geometric and topological parameters obtained after applying four different H-atom models in multipolar refinement on high-resolution X-ray data only were compared with the results obtained for a reference joint high-resolution X-ray/neutron refinement. The geometry and the topological critical point and integrated parameters closest to the reference values were obtained after a mixed refinement (high-order refinement of heavy atoms, low-angle refinement of H atoms and elongation of the X,H distance to the average neutron bond lengths) supplemented by an estimation of the anisotropic thermal motions of H atoms using the SHADE program. Such a procedure works very well even for strong hydrogen bonds. The worst fit to the reference results for both critical point and integrated parameters was obtained when only the standardization to the average neutron X,H distances was applied. The non-H-atom parameters are also systematically influenced by the H-atom modeling. In order to compare topological and integrated properties calculated for H and non-H atoms in multipolar refinement when there are no neutron data, the same treatment of H atoms (ideally the mixed refinement + estimated anisotropic atomic displacement parameters for H atoms) should be applied. [source] Hexagonal high-temperature form of aluminium phosphate tridymite from X-ray powder dataACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2001Heribert A. Graetsch Similar to silica tridymite, AlPO4 tridymite shows a sequence of displacive phase transitions resulting in a dynamically disordered hexagonal high-temperature modification. Rietveld refinement reveals that the thermal motions of the tetrahedra can be described either by strongly anisotropic displacement parameters for oxygen or by split O atoms. Due to the ordered distribution of aluminium and phosphorus over alternating tetrahedra, the space group symmetry of high-temperature AlPO4 tridymite is reduced with respect to SiO2 tridymite from P63/mmc to P63mc. [source] | |||||||||||||